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Zimmer RK, Ferrier GA, Zimmer CA. Chemosensory Exploitation and Predator-Prey Arms Races. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.752327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Thousands of armed predatory species, distributed widely across the metazoan tree-of-life, consume only hard-shell or exoskeleton-bearing organisms (called “durophagy”). Prey armor clearly has evolved in response to selection by predators, but there is little evidence of the contrary, counter-adaptation by predators. Evolved consumer responses to prey, in general, might be more readily expressed in ways other than morphological traits, including via sensory cues. Here, we explored the chemosensory basis for durophagy in a model predator-prey system, and identified intimate associations between durophagous predators and their shelled prey. Barnacles (Balanus glandula and Semibalanus cariosus) bear hard shells and secrete, respectively, a 199 or 201 kDa glycoprotein ortholog (named “MULTIFUNCin”), with expression limited to the body armor (epidermis, cuticle, and live shell). To test for effects of MULTIFUNCin on predators, we constructed faux prey to mimic meaningful physical and chemical characteristics of live barnacles. In separate experiments, each consumer species was presented MULTIFUNCin, purified from either B. glandula or S. cariosus, at a typical armor concentration. All six predatory species (sea star, Pisaster ochraceus; whelks, Acanthinucella spirata, Nucella emarginata, N. ostrina, N. canaliculata, and N. lamellosa) attacked and ate MULTIFUNCin-infused faux prey significantly more than controls. Akin to barnacles, secretion of glycoprotein-rich extracellular matrices is common among armored prey species—from marine sponges to terrestrial vertebrates. Our results, therefore, suggest that chemosensory exploitation of glycoproteins could be widespread, with notable consequences for life on land and in the sea.
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Ghosh S, Ahmad R, Banerjee K, AlAjmi MF, Rahman S. Mechanistic Aspects of Microbe-Mediated Nanoparticle Synthesis. Front Microbiol 2021; 12:638068. [PMID: 34025600 PMCID: PMC8131684 DOI: 10.3389/fmicb.2021.638068] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 03/25/2021] [Indexed: 11/13/2022] Open
Abstract
In recent times, nanoparticles (NPs) have found increasing interest owing to their size, large surface areas, distinctive structures, and unique properties, making them suitable for various industrial and biomedical applications. Biogenic synthesis of NPs using microbes is a recent trend and a greener approach than physical and chemical methods of synthesis, which demand higher costs, greater energy consumption, and complex reaction conditions and ensue hazardous environmental impact. Several microorganisms are known to trap metals in situ and convert them into elemental NPs forms. They are found to accumulate inside and outside of the cell as well as in the periplasmic space. Despite the toxicity of NPs, the driving factor for the production of NPs inside microorganisms remains unelucidated. Several reports suggest that nanotization is a way of stress response and biodefense mechanism for the microbe, which involves metal excretion/accumulation across membranes, enzymatic action, efflux pump systems, binding at peptides, and precipitation. Moreover, genes also play an important role for microbial nanoparticle biosynthesis. The resistance of microbial cells to metal ions during inward and outward transportation leads to precipitation. Accordingly, it becomes pertinent to understand the interaction of the metal ions with proteins, DNA, organelles, membranes, and their subsequent cellular uptake. The elucidation of the mechanism also allows us to control the shape, size, and monodispersity of the NPs to develop large-scale production according to the required application. This article reviews different means in microbial synthesis of NPs focusing on understanding the cellular, biochemical, and molecular mechanisms of nanotization of metals.
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Affiliation(s)
- Shubhrima Ghosh
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, India
- Research and Development Office, Ashoka University, Sonepat, India
| | - Razi Ahmad
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, India
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Kamalika Banerjee
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Mohamed Fahad AlAjmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Shakilur Rahman
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
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3
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Skeffington AW, Donath A. ProminTools: shedding light on proteins of unknown function in biomineralization with user friendly tools illustrated using mollusc shell matrix protein sequences. PeerJ 2020; 8:e9852. [PMID: 32974096 PMCID: PMC7489238 DOI: 10.7717/peerj.9852] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 08/11/2020] [Indexed: 01/24/2023] Open
Abstract
Biominerals are crucial to the fitness of many organism and studies of the mechanisms of biomineralization are driving research into novel materials. Biomineralization is generally controlled by a matrix of organic molecules including proteins, so proteomic studies of biominerals are important for understanding biomineralization mechanisms. Many such studies identify large numbers of proteins of unknown function, which are often of low sequence complexity and biased in their amino acid composition. A lack of user-friendly tools to find patterns in such sequences and robustly analyse their statistical properties relative to the background proteome means that they are often neglected in follow-up studies. Here we present ProminTools, a user-friendly package for comparison of two sets of protein sequences in terms of their global properties and motif content. Outputs include data tables, graphical summaries in an html file and an R-script as a starting point for data-set specific visualizations. We demonstrate the utility of ProminTools using a previously published shell matrix proteome of the giant limpet Lottia gigantea.
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Affiliation(s)
| | - Andreas Donath
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
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4
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Nudelman H, Lee YZ, Hung YL, Kolusheva S, Upcher A, Chen YC, Chen JY, Sue SC, Zarivach R. Understanding the Biomineralization Role of Magnetite-Interacting Components (MICs) From Magnetotactic Bacteria. Front Microbiol 2018; 9:2480. [PMID: 30405554 PMCID: PMC6206293 DOI: 10.3389/fmicb.2018.02480] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 09/28/2018] [Indexed: 11/20/2022] Open
Abstract
Biomineralization is a process that takes place in all domains of life and which usually helps organisms to harden soft tissues by creating inorganic structures that facilitate their biological functions. It was shown that biominerals are under tight biological control via proteins that are involved in nucleation initiation and/or which act as structural skeletons. Magnetotactic bacteria (MTB) use iron biomineralization to create nano-magnetic particles in a specialized organelle, the magnetosome, to align to the geomagnetic field. A specific set of magnetite-associated proteins (MAPs) is involved in regulating magnetite nucleation, size, and shape. These MAPs are all predicted to contain specific 17–22 residue-long sequences involved in magnetite formation. To understand the mechanism of magnetite formation, we focused on three different MAPs, MamC, Mms6 and Mms7, and studied the predicted iron-binding sequences. Using nuclear magnetic resonance (NMR), we differentiated the recognition mode of each MAP based on ion specificity, affinity, and binding residues. The significance of critical residues in each peptide was evaluated by mutation followed by an iron co-precipitation assay. Among the peptides, MamC showed weak ion binding but created the most significant effect in enhancing magnetite particle size, indicating the potency in controlling magnetite particle shape and size. Alternatively, Mms6 and Mms7 had strong binding affinities but less effect in modulating magnetite particle size, representing their major role potentially in initiating nucleation by increasing local metal concentration. Overall, our results explain how different MAPs affect magnetite synthesis, interact with Fe2+ ions and which residues are important for the MAPs functions.
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Affiliation(s)
- Hila Nudelman
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Yi-Zong Lee
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.,Instrumentation Center, National Tsing Hua University, Hsinchu, Taiwan
| | - Yi-Lin Hung
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.,Instrumentation Center, National Tsing Hua University, Hsinchu, Taiwan
| | - Sofiya Kolusheva
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Alexander Upcher
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Yi-Chen Chen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Jih-Ying Chen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Shih-Che Sue
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Raz Zarivach
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel.,Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
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Mosayebi J, Kiyasatfar M, Laurent S. Synthesis, Functionalization, and Design of Magnetic Nanoparticles for Theranostic Applications. Adv Healthc Mater 2017; 6. [PMID: 28990364 DOI: 10.1002/adhm.201700306] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 06/14/2017] [Indexed: 12/13/2022]
Abstract
In order to translate nanotechnology into medical practice, magnetic nanoparticles (MNPs) have been presented as a class of non-invasive nanomaterials for numerous biomedical applications. In particular, MNPs have opened a door for simultaneous diagnosis and brisk treatment of diseases in the form of theranostic agents. This review highlights the recent advances in preparation and utilization of MNPs from the synthesis and functionalization steps to the final design consideration in evading the body immune system for therapeutic and diagnostic applications with addressing the most recent examples of the literature in each section. This study provides a conceptual framework of a wide range of synthetic routes classified mainly as wet chemistry, state-of-the-art microfluidic reactors, and biogenic routes, along with the most popular coating materials to stabilize resultant MNPs. Additionally, key aspects of prolonging the half-life of MNPs via overcoming the sequential biological barriers are covered through unraveling the biophysical interactions at the bio-nano interface and giving a set of criteria to efficiently modulate MNPs' physicochemical properties. Furthermore, concepts of passive and active targeting for successful cell internalization, by respectively exploiting the unique properties of cancers and novel targeting ligands are described in detail. Finally, this study extensively covers the recent developments in magnetic drug targeting and hyperthermia as therapeutic applications of MNPs. In addition, multi-modal imaging via fusion of magnetic resonance imaging, and also innovative magnetic particle imaging with other imaging techniques for early diagnosis of diseases are extensively provided.
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Affiliation(s)
- Jalal Mosayebi
- Department of Mechanical Engineering; Urmia University; Urmia 5756151818 Iran
| | - Mehdi Kiyasatfar
- Department of Mechanical Engineering; Urmia University; Urmia 5756151818 Iran
| | - Sophie Laurent
- Laboratory of NMR and Molecular Imaging; University of Mons; Mons Belgium
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Sarem M, Lüdeke S, Thomann R, Salavei P, Zou Z, Habraken W, Masic A, Shastri VP. Disordered Conformation with Low Pii Helix in Phosphoproteins Orchestrates Biomimetic Apatite Formation. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2017; 29:1701629. [PMID: 28714191 DOI: 10.1002/adma.201701629] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 05/18/2017] [Indexed: 06/07/2023]
Abstract
The interplay between noncollagenous proteins and biomineralization is widely accepted, yet the contribution of their secondary structure in mineral formation remains to be clarified. This study demonstrates a role for phosvitin, an intrinsically disordered phosphoprotein, in chick embryo skeletal development, and using circular dichroism and matrix least-squares Henderson-Hasselbalch global fitting, unravels three distinct pH-dependent secondary structures in phosvitin. By sequestering phosvitin on a biomimetic 3D insoluble cationic framework at defined pHs, access is gained to phosvitin in various conformational states. Induction of biomimetic mineralization at near physiological conditions reveals that a disordered secondary structure with a low content of PII helix is remarkably efficient at promoting calcium adsorption, and results in the formation of biomimetic hydroxyapatite through an amorphous calcium phosphate precursor. By extending this finding to phosphorylated full-length human recombinant dentin matrix protein-1 (17-513 AA), this bioinspired approach provides compelling evidence for the role of a disordered secondary structure in phosphoproteins in bone-like apatite formation.
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Affiliation(s)
- Melika Sarem
- Institute for Macromolecular Chemistry, BIOSS Centre for Biological Signaling Studies, University of Freiburg, 79104, Freiburg, Germany
- Helmholtz Virtual Institute, Multifunctional Biomaterials for Medicine, Kantstr. 55, 14513, Teltow, Germany
| | - Steffen Lüdeke
- Institute of Pharmaceutical Sciences, University of Freiburg, 79104, Freiburg, Germany
| | - Ralf Thomann
- Institute for Macromolecular Chemistry, University of Freiburg, 79104, Freiburg, Germany
| | - Pavel Salavei
- BIOSS Toolbox, Centre for Biological Signaling Studies, University of Freiburg, 79104, Freiburg, Germany
| | - Zhaoyong Zou
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, Science Park Golm, 14424, Potsdam, Germany
| | - Wouter Habraken
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, Science Park Golm, 14424, Potsdam, Germany
| | - Admir Masic
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02149, USA
| | - V Prasad Shastri
- Institute for Macromolecular Chemistry, BIOSS Centre for Biological Signaling Studies, University of Freiburg, 79104, Freiburg, Germany
- Helmholtz Virtual Institute, Multifunctional Biomaterials for Medicine, Kantstr. 55, 14513, Teltow, Germany
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7
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Schauer KL, LeMoine CMR, Pelin A, Corradi N, Warren WC, Grosell M, McDonald MD. A proteinaceous organic matrix regulates carbonate mineral production in the marine teleost intestine. Sci Rep 2016; 6:34494. [PMID: 27694946 PMCID: PMC5046086 DOI: 10.1038/srep34494] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 09/14/2016] [Indexed: 12/24/2022] Open
Abstract
Marine teleost fish produce CaCO3 in their intestine as part of their osmoregulatory strategy. This precipitation is critical for rehydration and survival of the largest vertebrate group on earth, yet the molecular mechanisms that regulate this reaction are unknown. Here, we isolate and characterize an organic matrix associated with the intestinal precipitates produced by Gulf toadfish (Opsanus beta). Toadfish precipitates were purified using two different methods, and the associated organic matrix was extracted. Greater than 150 proteins were identified in the isolated matrix by mass spectrometry and subsequent database searching using an O. beta transcriptomic sequence library produced here. Many of the identified proteins were enriched in the matrix compared to the intestinal fluid, and three showed no substantial homology to any previously characterized protein in the NCBI database. To test the functionality of the isolated matrix, a micro-modified in vitro calcification assay was designed, which revealed that low concentrations of isolated matrix substantially promoted CaCO3 production, where high concentrations showed an inhibitory effect. High concentrations of matrix also decreased the incorporation of magnesium into the forming mineral, potentially providing an explanation for the variability in magnesium content observed in precipitates produced by different fish species.
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Affiliation(s)
- Kevin L Schauer
- Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, 33149, USA
| | - Christophe M R LeMoine
- Department of Biology, Brandon University, Brandon, MB, R7A 6A9, Canada.,Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Adrian Pelin
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Nicolas Corradi
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, Missouri 63108, USA
| | - Martin Grosell
- Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, 33149, USA
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Zhang H, Liu X, Feng S, Wang W, Schmidt-Rohr K, Akinc M, Nilsen-Hamilton M, Vaknin D, Mallapragada S. Morphological transformations in the magnetite biomineralizing protein Mms6 in iron solutions: a small-angle X-ray scattering study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:2818-2825. [PMID: 25669122 DOI: 10.1021/la5044377] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Magnetotactic bacteria that produce magnetic nanocrystals of uniform size and well-defined morphologies have inspired the use of biomineralization protein Mms6 to promote formation of uniform magnetic nanocrystals in vitro. Small angle X-ray scattering (SAXS) studies in physiological solutions reveal that Mms6 forms compact globular three-dimensional (3D) micelles (approximately 10 nm in diameter) that are, to a large extent, independent of concentration. In the presence of iron ions in the solutions, the general micellar morphology is preserved, however, with associations among micelles that are induced by iron ions. Compared with Mms6, the m2Mms6 mutant (with the sequence of hydroxyl/carboxyl containing residues in the C-terminal domain shuffled) exhibits subtle morphological changes in the presence of iron ions in solutions. The analysis of the SAXS data is consistent with a hierarchical core-corona micellar structure similar to that found in amphiphilic polymers. The addition of ferric and ferrous iron ions to the protein solution induces morphological changes in the micellar structure by transforming the 3D micelles into objects of reduced dimensionality of 2, with fractal-like characteristics (including Gaussian-chain-like) or, alternatively, platelet-like structures.
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Affiliation(s)
- Honghu Zhang
- Division of Materials Science and Engineering, Ames Laboratory, USDOE , Ames, Iowa 50011, United States
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Kashyap S, Woehl TJ, Liu X, Mallapragada SK, Prozorov T. Nucleation of iron oxide nanoparticles mediated by Mms6 protein in situ. ACS NANO 2014; 8:9097-9106. [PMID: 25162493 DOI: 10.1021/nn502551y] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Biomineralization proteins are widely used as templating agents in biomimetic synthesis of a variety of organic-inorganic nanostructures. However, the role of the protein in controlling the nucleation and growth of biomimetic particles is not well understood, because the mechanism of the bioinspired reaction is often deduced from ex situ analysis of the resultant nanoscale mineral phase. Here we report the direct visualization of biomimetic iron oxide nanoparticle nucleation mediated by an acidic bacterial recombinant protein, Mms6, during an in situ reaction induced by the controlled addition of sodium hydroxide to solution-phase Mms6 protein micelles incubated with ferric chloride. Using in situ liquid cell scanning transmission electron microscopy we observe the liquid iron prenucleation phase and nascent amorphous nanoparticles forming preferentially on the surface of protein micelles. Our results provide insight into the early steps of protein-mediated biomimetic nucleation of iron oxide and point to the importance of an extended protein surface during nanoparticle formation.
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Affiliation(s)
- Sanjay Kashyap
- Ames Laboratory, U.S. Department of Energy , Ames, Iowa 50011, United States
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Integrated self-assembly of the Mms6 magnetosome protein to form an iron-responsive structure. Int J Mol Sci 2013; 14:14594-606. [PMID: 23857056 PMCID: PMC3742261 DOI: 10.3390/ijms140714594] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 06/09/2013] [Accepted: 07/03/2013] [Indexed: 12/15/2022] Open
Abstract
A common feature of biomineralization proteins is their self-assembly to produce a surface consistent in size with the inorganic crystals that they produce. Mms6, a small protein of 60 amino acids from Magnetospirillum magneticum strain AMB-1 that promotes the in vitro growth of superparamagnetic magnetite nanocrystals, assembles in aqueous solution to form spherical micelles that could be visualized by TEM and AFM. The results reported here are consistent with the view that the N and C-terminal domains interact with each other within one polypeptide chain and across protein units in the assembly. From studies to determine the amino acid residues important for self-assembly, we identified the unique GL repeat in the N-terminal domain with additional contributions from amino acids in other positions, throughout the molecule. Analysis by CD spectroscopy identified a structural change in the iron-binding C-terminal domain in the presence of Fe3+. A change in the intrinsic fluorescence of tryptophan in the N-terminal domain showed that this structural change is transmitted through the protein. Thus, self-assembly of Mms6 involves an interlaced structure of intra- and inter-molecular interactions that results in a coordinated structural change in the protein assembly with iron binding.
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